Accounting for spatial sampling patterns in Bayesian phylogeography

Statistical phylogeography provides useful tools to characterize and quantify the spread of organisms during the course of evolution. Analyzing georeferenced genetic data often relies on the assumption that samples are preferentially collected in densely populated areas of the habitat. Deviation from this assumption negatively impacts the inference of the spatial and demographic dynamics. This issue is pervasive in phylogeography. It affects analyses that approximate the habitat as a set of discrete demes as well as those that treat it as a continuum. The present study introduces a Bayesian modeling approach that explicitly accommodates for spatial sampling strategies. An original inference technique, based on recent advances in statistical computing, is then described that is most suited to modeling data where sequences are preferentially collected at certain locations, independently of the outcome of the evolutionary process. The analysis of georeferenced genetic sequences from the West Nile virus in North America along with simulated data shows how assumptions about spatial sampling may impact our understanding of the forces shaping biodiversity across time and space.

An R toolbox for score-based measurement invariance tests in IRT models

The detection of differential item functioning (DIF) is a central topic in psychometrics and educational measurement. In the past few years, a new family of score-based tests of measurement invariance has been proposed, which allows the detection of DIF along arbitrary person covariates in a variety of item response theory (IRT) models. This paper illustrates the application of these tests within the R system for statistical computing, making them accessible to a broad range of users. This presentation also includes IRT models for which these tests have not previously been investigated, such as the generalized partial credit model. The paper has three goals: First, we review the ideas behind score-based tests of measurement invariance. Second, we describe the implementation of these tests within the R system for statistical computing, which is based on the interaction of the R packages mirt, psychotools and strucchange. Third, we illustrate the application of this software and the interpretation of its output in two empirical datasets. The complete R code for reproducing our results is reported in the paper.

Ensuring Scalability of a Cognitive Multiple-Choice Test through the Mokken Package in R Programming Language

This study investigated the scalability of a cognitive multiple-choice test through the Mokken package in the R programming language for statistical computing. A 2019 mathematics West African Examinations Council (WAEC) instrument was used to gather data from randomly drawn K-12 participants (N = 2866; Male = 1232; Female = 1634; Mean age = 16.5 years) in Education District I, Lagos State, Nigeria. The results showed that the monotone homogeneity model (MHM) was consistent with the empirical dataset. However, it was observed that the test could not be scaled unidimensionally due to the low scalability of some items. In addition, the test discriminated well and had low accuracy for item-invariant ordering (IIO). Thus, items seriously violated the IIO property and scalability criteria when the HT coefficient was estimated. Consequently, the test requires modification in order to provide monotonic characteristics. This has implications for public examining bodies when endeavouring to assess the IIO assumption of their items in order to boost the validity of testing.

Quantitative assessment of photic phenomena in the presbyopia-correcting intraocular lens

This was a prospective study to evaluate the feasibility of the photic phenomena test (PPT) for quantifying glare, halo, and starburst. We compared two presbyopia-correcting intraocular lenses (IOLs), the Symfony IOL and the PanOptix IOL, as well as the monofocal Clareon IOL in 111 IOL-implanted eyes of 111 patients who underwent the PPT 1 month postoperatively. The reproducibility of photic phenomena with the PPT was assessed in 39 multifocal IOL-implanted eyes of 20 patients and among the examiners. Patients with ocular diseases, except for refractive errors, were excluded. The mean values of the groups were evaluated. Bland–Altman plots were used to analyze statistical data (Easy R version 1.37; R Foundation for Statistical Computing, Vienna, Austria). The PPT reproducibility assessment revealed no fixed bias or regressive significance. Reproducibility was confirmed. The glare size did not differ significantly between the Symfony, PanOptix, and Clareon groups. The halo size was significantly larger in the Symfony group (p < 0.01) than in the PanOptix group. The halo intensity was significantly brighter in the PanOptix group (p < 0.01) than in the Symfony group. In contrast, no halos were perceived in the Clareon group. The starburst size or intensity did not differ significantly between the Symfony, PanOptix, and Clareon groups. We identified the photic phenomenon related to various IOLs.

Distribuição e autocorrelação espacial dos casos de Tentativas de Suicídio por medicamentos em um município paraibano

Trata-se de um estudo observacional, analítico e transversal, de caráter quantitativo, realizado a partir de dados secundários provenientes do Sistema de Informação de Agravos de Notificação (SINAN). Objetivou-se analisar o padrão espacial dos casos de tentativas de suicídio por medicamentos no município de Campina Grande/PB, em 2019. Foi realizado estatística descritiva, assim como elaboração de mapas (Moran e Lisa) para a verificação da distribuição espacial dos casos em estudo. Realizou-se, também, mapa coroplético para demonstrar a ocorrência e a intensidade do fenômeno e Diagrama de Espalhamento de Moran, utilizando-se o Índice de Moran Global e o Índice de Moran Local, com auxílio do software estatístico gratuito The R Project for Statistical Computing. Para nortear a análise espacial, utilizou-se a variável “bairro”. A amostra totalizou 237 pacientes residentes na zona urbana de Campina Grande que tentaram suicídio através do uso de medicamentos. O perfil dos pacientes obedeceu o seguinte padrão: sexo feminino (79,7%), faixa etária de 20 a 39 anos (51,5%), escolaridade em nível fundamental (49,4%), solteiro (a) como estado civil (64,5%) e a maioria sendo estudante (42,2%), seguido de desempregado (a) (32,1%). Os bairros que apresentaram o maior número de casos foram: Malvinas (n=23), Bodocongó (n=21) e Serrotão (n=9). Por outro lado, os bairros Mirante, Cuités, Sandra Cavalcante, Louzeiro, Itararé e Velame não apresentaram ocorrências de casos de tentativas de suicídio através do uso de medicamentos. Assim, verificou-se que, no quesito global, não houve autocorrelação espacial significativa na região estudada, com Índice de Moran Global encontrado de 0,1210.

BIOLOGICAL SEXUAL PROFILE BASED ON LINEAR DIMENSIONS OF HUMERI AND FEMURS OF ADULT BRAZILIAN HUMAN SKELETONS

This research aimed to assess the predictive ability and applicability for sexual diagnosis of algorithms developed from measurements of humeri and femurs from skeletons belonging to the CEAF Identified Skeletal Collection of the University of Pernambuco, Brazil. The sample was composed of 483 humeri and 452 femurs, obtained from 401 skeletons, 208 male and 193 female, with ages ranging from 15 to 109 years. The variables used were the transverse and vertical diameters of the humeral and femoral heads and the epicondylar width of these bones. The data collected were analyzed using R software (version 3.6.1, R Foundation for Statistical Computing). Only the univariate logistic regressions were considered predictive, making it possible to estimate sex based on any single variable in this study. The accuracy ranged from 93.8% to 97.5% for the humerus evaluation and from 92.9% to 95.6% for femurs, with the transverse diameter of the right humeral head being the most dimorphic measurement. Therefore, it is inferred that the sexual dimorphism present in the measurements of the humeri and femurs of our sample is high and enables the classification of sex reliably and assertively using the algorithms created.

RCX – an R package adapting the Cytoscape Exchange format for biological networks

Motivation: The Cytoscape Exchange (CX) format is a JSON-based data structure designed for the transmission of biological networks using standard web technologies. It was developed by the network data exchange (NDEx), which itself serves as online commons to share and collaborate on biological networks. The Cytoscape software for the analysis and visualization of biological networks contributes further elements to capture the visual layout within the CX format. However, there is a fundamental difference between web standards and R of how data has to be structured. Results: Here we present a software package to create, handle, validate, visualize and convert networks in CX format to standard data types and objects within R. Networks in this format can serve as a source for biological knowledge, and also capture the results of the analysis of those while preserving the visual layout across all platforms. The RCX package connects the R environment for statistical computing with platforms for collaboration, analysis and visualization of biological networks. Availability: RCX is a free and open-source R package, available via GitHub (https://github.com/frankkramer-lab/RCX) and submitted to Bioconductor.